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scran (version 1.0.3)

Methods for Single-Cell RNA-Seq Data Analysis

Description

This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.

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Version

Version

1.0.3

License

GPL-3

Maintainer

Aaron Lun

Last Published

February 15th, 2017

Functions in scran (1.0.3)

Spike-in normalization

Normalization with spike-in counts
Normalized Expression

Compute normalized expression values
Distance-to-median

Compute the distance-to-median statistic
Get spikes

Construct the spike-in matrix
Quick clustering

Quick clustering of cells
sandbag

Cell cycle phase training
decomposeVar

Decompose the gene-level variance
Deconvolution Methods

Normalization by deconvolution
correlatePairs

Test for significant correlations
convertTo

Convert to other classes
testVar

Test for significantly large variances
cyclone

Cell cycle phase classification
trendVar

Get the biological variability